RetrogeneDB ID: retro_eeur_328

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_255590:83..559(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003063
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSEEUG00000004638
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_eeur_328
ATCGTGGGCCCTGATGCTGCAGGGAAAGACCACCATCCTGTACAAAATTGAAATTGAGGTGAAATTGTGACCCACCATTC
CCACTACCGGCTTCAAACGTAGAAACTGTGGAGTACAAGGACATCAGTTTCACCGTGTGGGGATGTGGGTAGCCCAGGAC
AAGATCCGGCCTCTGTGGGCGCCACTACTTCCCAGAACACCACAAAGTCTGATCTCTGTGGTTGACAGCAAATGACAGAG
AGCGTGTGAACGAGGCCTGTGAGGAGCTCATGAGGATGTTGGCTGAAGATGAGCTCAGGGATGCCGTTCTGCTTGTGTTC
GCTAATAAGCAGGATCTTCCTAATGCCATGAATGCGGCTGAGATCACGGACAAGCTGGGCCTGCACTCCCTGCGCCACAG
GAACCGGTACATTCAGGCCACCTGTGCCACCAGCGGGGATGGGCTCTATGAGGGACTGGACTGGCTCCGGAACCAG

Alignment

ORF - retro_eeur_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 85.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  MVGLDAAGK-TTILYK-LKL-GEIVT-TIPTIGF-NVETVEYKNISFTVW-DVGG-QDKIRPLW-RHYF-
          .VG.DAAGK.TTILYK.LKL.GEIVT.TIPT.GF.NVETVEYK.ISFTVW.DVG..QDKIRPLW.RHYF.
Retrocopy IVGPDAAGK>TTILYK>LKL>GEIVT>TIPTTGF>NVETVEYKDISFTVW>DVGS>QDKIRPLW>RHYF>

Parental  QNT-QGLIFVVDS-NDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRH
          QNT.Q.LI.VVDS.NDRERVNEA.EELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRH
Retrocopy QNT>QSLISVVDS>NDRERVNEACEELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRH

Parental  RNWYIQATCATSGDGLYEGLDWLSNQ
          RN.YIQATCATSGDGLYEGLDWL.NQ
Retrocopy RNRYIQATCATSGDGLYEGLDWLRNQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	139.39 RPM
SRP017611_kidney	0.00 RPM	212.48 RPM
SRP017611_liver	0.00 RPM	81.51 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_328 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328 , retro_eeur_660, retro_eeur_684, retro_eeur_76,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,